Microarray Information





Microarray Intensity Plot





QC Metrics


MAPD : Good < 0.20 ; Acceptable < 0.25
SNPQC : Good >= 26
WavinessSd : Good < 0.12




CNA Genomic Plots

Normalized, centered, segmented and called.

L2R + BAF

L2R

BAF





CNA Karyotypic Plot

Normalized, centered, segmented and called.





Genomic Instability Metrics Table





Segments Table

Any value (including gene symbols) can be queried in the ‘Search’ box. To search for an exact symbol try adding a coma (,) at the end of your query. Case is insensitive.

L2R

BAF





Target Genes Table

Any value can be queried in the ‘Search’ box. Case is insensitive.





Truncated Genes Table

Any value can be queried in the ‘Search’ box. Case is insensitive.

Blank cells correspond to genomic regions for which BAF is non-determined (no covering probe, thus no BAF segment).

Found 37 truncated gene(s).





CNA Chromosomal Plots

Normalized, centered, segmented and called.

chr1

chr2

chr3

chr4

chr5

chr6

chr7

chr8

chr9

chr10

chr11

chr12

chr13

chr14

chr15

chr16

chr17

chr18

chr19

chr20

chr21

chr22

chrX

chrY





Miscellaneous Information

R Session Info

## R version 4.1.2 (2021-11-01)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 17763)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                   LC_TIME=French_France.1252    
## 
## attached base packages:
##  [1] parallel  stats4    splines   stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 apt.oncoscan.2.4.0_0.1.6          sequenza_3.0.0                    seqinr_4.2-8                     
##  [5] rhdf5_2.38.0                      R.utils_2.11.0                    R.oo_1.24.0                       R.methodsS3_1.8.1                
##  [9] mclust_5.4.9                      iotools_0.3-2                     DT_0.21                           dplyr_1.0.8                      
## [13] changepoint_2.2.2                 zoo_1.8-9                         BSgenome_1.62.0                   rtracklayer_1.54.0               
## [17] Biostrings_2.62.0                 XVector_0.34.0                    aroma.light_3.24.0                affxparser_1.66.0                
## [21] ASCAT_3.0.0                       doParallel_1.0.17                 iterators_1.0.14                  foreach_1.5.2                    
## [25] GenomicRanges_1.46.1              GenomeInfoDb_1.30.1               IRanges_2.28.0                    S4Vectors_0.32.3                 
## [29] data.table_1.14.2                 RColorBrewer_1.1-2                EaCoN_0.3.6-2                     CGHbase_1.54.0                   
## [33] marray_1.72.0                     limma_3.50.1                      Biobase_2.54.0                    BiocGenerics_0.40.0              
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-7                matrixStats_0.61.0          bslib_0.3.1                 tools_4.1.2                 utf8_1.2.2                 
##  [6] R6_2.5.1                    DBI_1.1.2                   rhdf5filters_1.6.0          ade4_1.7-18                 tidyselect_1.1.2           
## [11] compiler_4.1.2              cli_3.1.1                   DelayedArray_0.20.0         sass_0.4.0                  readr_2.1.2                
## [16] pbapply_1.5-0               stringr_1.4.0               digest_0.6.29               Rsamtools_2.10.0            rmarkdown_2.12             
## [21] pkgconfig_2.0.3             htmltools_0.5.2             MatrixGenerics_1.6.0        fastmap_1.1.0               htmlwidgets_1.5.4          
## [26] rlang_1.0.1                 rstudioapi_0.13             jquerylib_0.1.4             BiocIO_1.4.0                generics_0.1.2             
## [31] jsonlite_1.8.0              crosstalk_1.2.0             BiocParallel_1.28.3         RCurl_1.98-1.6              magrittr_2.0.2             
## [36] GenomeInfoDbData_1.2.7      Matrix_1.4-0                Rhdf5lib_1.16.0             fansi_1.0.2                 lifecycle_1.0.1            
## [41] stringi_1.7.6               yaml_2.3.5                  oncoscanR_0.1.1             MASS_7.3-55                 SummarizedExperiment_1.24.0
## [46] zlibbioc_1.40.0             grid_4.1.2                  crayon_1.5.0                lattice_0.20-45             hms_1.1.1                  
## [51] seqminer_8.4                knitr_1.37                  pillar_1.7.0                rjson_0.2.21                codetools_0.2-18           
## [56] XML_3.99-0.9                glue_1.6.1                  evaluate_0.15               squash_1.0.9                copynumber_1.34.0          
## [61] vctrs_0.3.8                 tzdb_0.2.0                  purrr_0.3.4                 assertthat_0.2.1            xfun_0.30                  
## [66] restfulr_0.0.13             tibble_3.1.6                GenomicAlignments_1.30.0    ellipsis_0.3.2

Data summary

EaCoN Parameters

Affymetrix Parameters